How to use anvio's gzipped HMM externally with HMMER?
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2.6 years ago
O.rka ▴ 540

I'm trying to use this HMM that I have with my installation of Anvio using just HMMER: https://github.com/merenlab/anvio/blob/master/anvio/data/hmm/Bacteria_71/genes.hmm.gz

I've went through the source code below but it's not very clear how it's running: https://github.com/merenlab/anvio/blob/master/bin/anvi-run-hmms

The only way I can get this to run is by gzipping, then pressing the HMM, and then using hmmscan. Is this the only way to run HMMER? I'm not sure if Anvio decompresses and presses the HMM each time it is running.

Also, if you're running a set of HMMs against the proteome of a single organism, should you use HMMSCAN or HMMSEARCH?

anvio binning hmm • 719 views
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Entering edit mode
2.6 years ago
h.mon 34k

I am not completely sure, but yes, it seems Anvi'o decompresses the profiles to a temporary folder, presses them and then runs hmmscan. The file you want to look at is https://github.com/merenlab/anvio/blob/master/anvio/drivers/hmmer.py

Also, if you're running a set of HMMs against the proteome of a single organism, should you use HMMSCAN or HMMSEARCH?

hmmscan vs. hmmsearch speed: the numerology

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